This script runs prequisite data importing/cleaning scripts necessary for almost all other analyses.
Three Rivers databases and files are ingested with two scripts:
Scripts/1_Data_Import.R: imports the bird and
vegetation survey databases maintained by Three Rivers (.accdb format)
into R. Each table in the databases is imported as its own data frame
object.
Scripts/2_Spatial_Data_Import.R: imports Three
Rivers spatial data maintained in Three Rivers geodatabases into R. Each
feature class becomes an sf data frame object.
library(here)
source(here("Scripts", "1_Data_Import.R"))
source(here("Scripts", "2_Spatial_Data_Import.R"))Note: to update the files/databases used in these analyses update the file paths in the data import scripts.
The data imported by 1_Data_Import.R include the
following files:
The data imported by 2_Spatial_Data_Import.R include the
following files:
Data are further processed with a data cleaning script
(Scripts/3_Data_Cleaning.R) before being fed into
subsequent analyses. Cleaning steps include:
Spatial burn management unit data: tidy park names; add missing year planted dates
Spatial bird survey transects: tidy park names; create spatial transects for surveys that do not have spatial data
MLCCS habitat types: align spelling/styling of categories across current and future layers
Note: many of the fixes made by cleaning script should eventually be applied to the original data files, but for now are done programatically for
Scripts/4_Covariate_Data_Prep.R is run to prepare
assorted environmental data for use in other analyses. Specifically, the
script prepares the following objects:
area_by_year: cumulative total area of restored grasslands at Crow-Hassan by year
spring_precip: spring precipitation at Crow-Hassan by year from PRISM data
burns: a tidied and “long” version of the master burn spreadsheet indicating which units were burned in which years.
Scripts/5_Prep_Species.R aligns the TRPD bird species
table with the eBird taxonomy, which facilitates combination/comparison
with other datasets. The script also importa the Avian Conservation
Assessment Database and MN BBA species lists (with habitat
associations), which are used to generate a list of grassland
species.
By Sam Safran